The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition

Ray, Suprabhat; Kreitler, D.F.; Gulick, Andrew M.; Murkin, Andrew S.

doi:10.1021/acschembio.8b00225

Cited by 31 publications

(36 citation statements)

References 16 publications

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“…The inverse SKIE was attributed to an SEIE arising from the rapid equilibrium of thiolate formation prior to binding of succinate, while the normal SKIE was attributed to the downstream transfer of a solvent-derived hydron, presumably involved in protonation of the carbonyl oxygen of glyoxylate. Interestingly, an inverse SKIE of 0.40 ± 0.03 was also measured on k inact /K I for 3-nitropropionate [10], a succinate analogue that reacts covalently with Cys191, a result that can be attributed to the same pre-binding equilibrium and a requirement for the minor thiolate form [21].…”

Section: Isocitrate Lyasementioning

confidence: 89%

Inverse Solvent Isotope Effects in Enzyme-Catalyzed Reactions

Fernandez

Murkin

2020

Molecules

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Solvent isotope effects have long been used as a mechanistic tool for determining enzyme mechanisms. Most commonly, macroscopic rate constants such as k cat and k cat /K m are found to decrease when the reaction is performed in D 2 O for a variety of reasons including the transfer of protons. Under certain circumstances, these constants are found to increase, in what is termed an inverse solvent kinetic isotope effect (SKIE), which can be a diagnostic mechanistic feature. Generally, these phenomena can be attributed to an inverse solvent equilibrium isotope effect on a rapid equilibrium preceding the rate-limiting step(s). This review surveys inverse SKIEs in enzyme-catalyzed reactions by assessing their underlying origins in common mechanistic themes. Case studies for each category are presented, and the mechanistic implications are put into context. It is hoped that readers may find the illustrative examples valuable in planning and interpreting solvent isotope effect experiments.

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Section: Isocitrate Lyasementioning

confidence: 89%

Inverse Solvent Isotope Effects in Enzyme-Catalyzed Reactions

Fernandez

Murkin

2020

Molecules

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“…Formation of a thiohydroximate adduct in the reaction of a nitro group with a cysteine residue in the active site has been reported. 47 In fragment screening conducted prior to the COVID Moonshot project, 48 an electrophile library 49,50 oriented toward covalent bonding was used. As these electrophile libraries did not cover nitro groups, they evaluated a different chemical space from that examined in the present study.…”

Section: Discussionmentioning

confidence: 99%

Screening for inhibitors of main protease in SARS-CoV-2: in silico and in vitro approach avoiding secondary amides

Sekijima

Yamamoto

Yasuo

2021

Preprint

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In addition to vaccines, antiviral drugs are essential for suppressing COVID-19.Although several inhibitor candidates were reported for SARS-CoV-2 main protease, most are highly polar peptidomimetics with poor oral bioavailability and cell membrane permeability. Here, we conducted structure-based virtual screening and in vitro assays to obtain hit compounds belonging to a new chemical space excluding secondary amides. In total, 180 compounds were subjected to the primary assay at 20 µM, and nine compounds with inhibition rates higher than 5% were obtained. The IC 50 of six compounds was determined in dose-response experiments, with the values on the order of 10 -4 µM. Although nitro groups were enriched in the substructure of the hit compounds, they did not significantly contribute to the binding interaction in 1 the predicted docking poses. Physicochemical properties prediction showed good oral absorption. These new scaffolds are promising candidates for future optimization.

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“…Several other ICL inhibitors have been identified, such as 3-bromopyruvate, 3-nitropropionate, and 2-vinyl-D-isocitrate [15][16][17]. However, these inhibitors display nonspecific hepatotoxicity, making them unsuitable as drug candidates [18].…”

Section: Introductionmentioning

confidence: 99%

2-Aminopyridine Analogs Inhibit Both Enzymes of the Glyoxylate Shunt in Pseudomonas aeruginosa

McVey

Bartlett

Kajbaf

et al. 2020

IJMS

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Pseudomonas aeruginosa is an opportunistic pathogen responsible for many hospital-acquired infections. P. aeruginosa can thrive in diverse infection scenarios by rewiring its central metabolism. An example of this is the production of biomass from C2 nutrient sources such as acetate via the glyoxylate shunt when glucose is not available. The glyoxylate shunt is comprised of two enzymes, isocitrate lyase (ICL) and malate synthase G (MS), and flux through the shunt is essential for the survival of the organism in mammalian systems. In this study, we characterized the mode of action and cytotoxicity of structural analogs of 2-aminopyridines, which have been identified by earlier work as being inhibitory to both shunt enzymes. Two of these analogs were able to inhibit ICL and MS in vitro and prevented growth of P. aeruginosa on acetate (indicating cell permeability). Moreover, the compounds exerted negligible cytotoxicity against three human cell lines and showed promising in vitro drug metabolism and safety profiles. Isothermal titration calorimetry was used to confirm binding of one of the analogs to ICL and MS, and the mode of enzyme inhibition was determined. Our data suggest that these 2-aminopyridine analogs have potential as anti-pseudomonal agents.

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The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition

Cited by 31 publications

References 16 publications

Inverse Solvent Isotope Effects in Enzyme-Catalyzed Reactions

Inverse Solvent Isotope Effects in Enzyme-Catalyzed Reactions

Screening for inhibitors of main protease in SARS-CoV-2: in silico and in vitro approach avoiding secondary amides

2-Aminopyridine Analogs Inhibit Both Enzymes of the Glyoxylate Shunt in Pseudomonas aeruginosa

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